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Can ArcGIS for Server remain online when performing a backup?
Yes, performing a backup of ArcGIS for Server while it is online is possible, however administrative changes to the site cannot be made when the backup is in progress.
There are two ways to perform a backup on ArcGIS for Server:
• Via ArcGIS for Server Backup Utility
• Via the ArcGIS for Server Admin endpoint
Expect a brief downtime of services when performing a backup of ArcGIS for Server 10.1 and prior.